19-44898511-CTT-CTTT

Variant names:

• chr19-44898511-C-CT
• rs34896370
• NM_001128917.2:c.644-2206dupT

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001128917.2(TOMM40):​c.644-2206dupT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.24 (1688 hom., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: TOMM40 NM_001128917.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.82
• Publications: 1 publications found

Genes affected

TOMM40 (HGNC:18001): (translocase of outer mitochondrial membrane 40) The protein encoded by this gene is localized in the outer membrane of the mitochondria. It is the channel-forming subunit of the translocase of the mitochondrial outer membrane (TOM) complex that is essential for import of protein precursors into mitochondria. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Aug 2015]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TOMM40	NM_001128917.2	c.644-2206dupT		intron_variant	Intron 5 of 8	ENST00000426677.7	NP_001122389.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TOMM40	ENST00000426677.7	c.644-2219_644-2218insT		intron_variant	Intron 5 of 8	1	NM_001128917.2	ENSP00000410339.1

Frequencies

GnomAD3 genomes AF: 0.235 AC: 22914 AN: 97464 Hom.: 1687 Cov.: 0

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.0684

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.0781

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.258

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.235 AC: 22915 AN: 97450 Hom.: 1688 Cov.: 0 AF XY: 0.224 AC XY: 10023 AN XY: 44686

African (AFR) AF: 0.220 AC: 5245 AN: 23862

American (AMR) AF: 0.157 AC: 1333 AN: 8480

Ashkenazi Jewish (ASJ) AF: 0.328 AC: 912 AN: 2780

East Asian (EAS) AF: 0.0686 AC: 238 AN: 3470

South Asian (SAS) AF: 0.241 AC: 678 AN: 2816

European-Finnish (FIN) AF: 0.0781 AC: 173 AN: 2216

Middle Eastern (MID) AF: 0.278 AC: 35 AN: 126

European-Non Finnish (NFE) AF: 0.267 AC: 13800 AN: 51648

Other (OTH) AF: 0.258 AC: 344 AN: 1332

Alfa AF: 0.170 Hom.: 259

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-1.8
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs34896370; hg19: chr19-45401768;